VcfRefGen

vcfRefGen is a tool for generating VCF reference panels for minimac imputation. It reduces VCF files by removing the info field, saving only the GT genotype field and removing any records where any kept sample is not phased or is missing a genotype.

Download

Source code can be found here .

Parameter

Parameter	Description
--in <filename>	Input VCF filename. The latest 1000 Genomes files can be found here.
--out <filename>	Output VCF filename.
--uncompress	write an uncompressed VCF output file.
--sampleSubset <filename>	filename of file with samples IDs to keep (one sample ID per line).
--minAC	minor allele count to keep.
--filterList <filename>	filename of file containing regions to include. format: start end start & end positions should be 1-based inclusive positions for SNPs start=end position
--params	print the parameter settings

Example

Please find below the command we used for generating MetaboChip specific reference panels from 1000 Genomes data:

   foreach chr (`seq 1 22`)

     runon -m 1024 vcfRefGen --in ALL.chr$chr.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \
               --out chr$chr.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz \
               --minAC 2 --filterList chr$chr.filter.regions
   end